bump dependencies, bump gradle to 8.7

Author: rdk

README.md

@@ -20,7 +20,7 @@ Version 2.4 adds support for `.cif` input and contains a special profile for pre
 
 ### Requirements
 
-* Java 8 to 20
+* Java 11 to 21
 * PyMOL 1.7 (or newer) for viewing visualizations (optional)
 
 P2Rank is tested on Linux, macOS, and Windows. 

build.gradle

@@ -164,20 +164,20 @@ tasks.named("dependencyUpdates").configure {
 
 dependencies {
 
-    implementation 'org.apache.groovy:groovy:4.0.20'
+    implementation 'org.apache.groovy:groovy:4.0.21'
 
     implementation 'org.codehaus.gpars:gpars:1.2.1'
     implementation 'org.apache.commons:commons-lang3:3.14.0'
     implementation 'org.apache.commons:commons-math3:3.6.1'
-    implementation 'commons-io:commons-io:2.16.0'
+    implementation 'commons-io:commons-io:2.16.1'
     implementation 'com.google.guava:guava:33.1.0-jre'
     implementation 'com.google.code.gson:gson:2.10.1'
     implementation 'com.univocity:univocity-parsers:2.9.1' // csv parser
     implementation 'org.apache.commons:commons-csv:1.10.0'
     implementation 'org.zeroturnaround:zt-zip:1.17'
     implementation 'org.apache.commons:commons-compress:1.26.1'
     implementation 'org.tukaani:xz:1.9'
-    implementation 'com.github.luben:zstd-jni:1.5.6-1'
+    implementation 'com.github.luben:zstd-jni:1.5.6-2'
     implementation 'com.github.dpaukov:combinatoricslib3:3.4.0'
 
     implementation 'org.slf4j:slf4j-api:1.7.36'

distro/README.md

@@ -20,7 +20,7 @@ Version 2.4 adds support for `.cif` input and contains a special profile for pre
 
 ### Requirements
 
-* Java 8 to 20
+* Java 11 to 22
 * PyMOL 1.7 (or newer) for viewing visualizations (optional)
 
 P2Rank is tested on Linux, macOS, and Windows. 

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.6-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.7-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

gradlew.bat

@@ -43,11 +43,11 @@ set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
 if %ERRORLEVEL% equ 0 goto execute
 
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail
 
@@ -57,11 +57,11 @@ set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
 if exist "%JAVA_EXE%" goto execute
 
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail
 

misc/tutorials/development-notes.md

@@ -1,6 +1,6 @@
 
 
-## Upgrade gradle weapper
+## Upgrade gradle wrapper
 
 ~~~sh
 ./gradlew wrapper --gradle-version latest